Contacts of the helix formed by residues 77 - 88 (chain B) in PDB entry 2VL3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B PRO* 6.1 1.1 - - + -
76B ASN* 1.3 77.2 - - - +
78B ALA* 1.3 62.8 + - - +
79B PHE* 3.1 16.0 + - + +
80B VAL* 3.0 34.2 + - - +
81B THR* 3.1 17.8 + - - +
98B ALA* 3.7 1.8 - - - -
100B PRO* 4.3 1.3 - - - +
42C ALA 5.1 1.4 - - - +
44C THR* 5.3 1.0 - - - +
76C ASN* 4.6 0.7 + - - -
119C ILE 3.4 23.3 - - - +
120C PHE* 3.9 25.8 + - + -
124C ARG* 2.7 31.1 + - - +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 3.6 24.8 - - + +
17B GLY 3.1 14.1 - - - +
18B GLU 3.5 34.8 - - - +
19B PRO* 3.7 8.0 - - + +
77B ASP* 1.3 72.0 - - - +
79B PHE* 1.3 60.4 + - - +
81B THR* 3.1 10.7 + - - +
82B GLY 2.9 24.9 + - - -
98B ALA* 3.6 5.5 - - + +
100B PRO* 5.4 0.4 - - - +
119C ILE 4.7 2.4 + - - -
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY 4.1 8.2 - - - +
18B GLU* 4.1 8.5 - - + -
19B PRO* 3.2 37.9 - - + -
77B ASP* 3.1 11.8 + - + +
78B ALA* 1.3 77.1 - - - +
80B VAL* 1.3 64.7 + - - +
82B GLY* 3.5 0.3 + - - -
83B GLU* 3.3 27.9 + - - +
86B ARG* 5.1 0.5 + - - -
42C ALA 4.9 0.4 - - - +
43C PHE* 3.9 19.3 - - - +
44C THR* 4.0 17.9 - - + -
45C PRO* 3.3 38.1 - - + -
119C ILE* 5.8 1.1 - - + -
120C PHE* 4.1 20.4 - + - -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 3.9 20.2 - - + -
43B PHE* 3.9 17.1 - - + -
76B ASN* 4.0 17.3 - - + +
77B ASP* 3.0 27.4 + - - +
79B PHE* 1.3 76.2 - - - +
81B THR* 1.3 62.9 + - - +
83B GLU* 3.4 4.9 + - - +
84B TRP* 3.0 20.4 + - - +
42C ALA 3.6 21.8 - - - +
43C PHE* 4.5 7.2 - - + -
76C ASN* 4.5 7.0 - - - +
80C VAL* 4.1 21.5 - - + -
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE 5.0 0.2 + - - -
17B GLY 4.6 2.8 + - - -
42B ALA* 4.7 4.3 - - + -
74B SER* 3.5 24.2 - - - +
76B ASN* 3.6 13.2 - - + -
77B ASP 3.1 10.8 + - - +
78B ALA* 3.1 21.8 + - - +
80B VAL* 1.3 77.8 - - - +
82B GLY* 1.3 55.1 + - - +
84B TRP* 3.3 9.2 + - + +
85B GLY 3.0 23.0 + - - -
96B LEU* 3.8 29.7 + - + +
97B LEU 4.5 2.5 - - - +
98B ALA* 3.5 21.7 + - + +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY* 4.0 13.7 - - - -
78B ALA 2.9 16.5 + - - -
79B PHE 4.0 0.7 - - - -
81B THR* 1.3 73.7 + - - +
83B GLU* 1.3 65.4 + - - +
85B GLY* 3.3 1.9 + - - -
86B ARG* 3.1 46.7 + - - -
96B LEU* 5.5 2.5 - - - -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE* 4.1 6.6 - - + -
79B PHE 3.3 17.0 + - - +
80B VAL 3.8 3.6 - - - +
82B GLY* 1.3 76.0 - - - +
84B TRP* 1.3 58.1 + - - +
86B ARG* 3.4 29.4 + - - +
87B ALA* 3.0 28.8 + - - +
43C PHE* 3.5 49.5 - - + +
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Residues in contact with TRP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 3.7 25.1 - - + -
42B ALA* 3.4 28.7 - - + -
43B PHE* 3.1 41.6 - + + +
47B CYS* 3.7 17.7 - - + -
48B SER* 2.8 36.6 - - - -
52B LEU* 3.7 24.2 - - + -
72B CYS* 4.1 13.2 - - - -
74B SER* 5.0 4.9 - - - -
80B VAL 3.0 18.1 + - - +
81B THR* 3.6 5.8 - - + +
82B GLY 3.2 0.4 - - - -
83B GLU* 1.3 76.1 - - - +
85B GLY* 1.3 59.9 + - - +
87B ALA* 3.4 2.1 + - - +
88B HIS* 3.3 37.6 + + - -
96B LEU* 3.6 29.8 - - + -
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU* 4.9 1.3 - - - -
81B THR 3.0 14.6 + - - -
82B GLY* 3.3 2.7 + - - -
84B TRP* 1.3 73.7 - - - +
86B ARG* 1.3 65.6 + - - +
88B HIS* 2.9 13.4 + - - -
89B LYS 2.9 10.9 + - - -
90B ALA* 3.1 22.1 + - - +
91B GLU 5.5 0.4 - - - -
96B LEU* 4.0 19.9 - - - +
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Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY* 4.2 15.2 + - - -
79B PHE 5.1 0.4 + - - -
82B GLY* 3.1 30.7 + - - +
83B GLU* 3.4 50.5 + - - +
85B GLY* 1.3 74.1 - - - +
87B ALA* 1.3 62.6 + - - +
89B LYS* 3.1 17.3 + - - +
90B ALA 5.1 0.2 - - - +
91B GLU 6.2 0.4 - - - +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE* 4.4 15.9 - - + -
83B GLU 3.0 17.6 + - - +
84B TRP* 3.5 10.8 - - - +
85B GLY 3.1 0.2 - - - -
86B ARG* 1.3 76.6 - - - +
88B HIS* 1.3 69.2 + - + +
89B LYS* 3.5 5.4 - - - +
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Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 5.7 1.6 - - - -
48B SER* 2.9 43.6 - - - -
52B LEU* 3.5 26.7 - - + -
53B PRO* 4.0 13.3 - - + +
56B VAL* 4.0 19.6 - - + +
84B TRP* 3.3 36.2 + + - -
85B GLY* 2.9 5.9 + - - +
87B ALA* 1.3 85.2 + - + +
89B LYS* 1.3 78.3 + - - +
90B ALA 3.2 2.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il